Hi,
On Sun, Jul 6, 2014 at 3:20 AM, Mele N. <nm10g13.soton.ac.uk> wrote:
> follow what you advice and run my analysis with AmberTools14 and
> everything work fine. I also add on the top of each run trajectory a fake
> line the first trajectory run. I don't really know where was the problem. I
> am a bit confused on the reason why it doesn't work with Amber13Tools.
>
It seems like your trajectories do not have a title line (see
http://ambermd.org/formats.html#trajectory for details). I think this can
happen if you are running with the '-A' command line flag but no trajectory
exists.
> Are you using ASCII or NetCDF trajectories?
>
> I use ASCII trajectories,
>
I highly recommend switching to NetCDF trajectories (ioutfm=1). They have
higher precision, are faster to process, and are far less error-prone than
ASCII trajectories. I also recommend NetCDF restarts (ntxo=2).
-Dan
>
>
> Many thanks for your help,
>
> Nawel
>
> -Dan
>
>
> >
> >
> > I don't know what is happening with my run after the first one, it is
> like
> > the files are not recognized.
> > It is really strange, because with another system everything goes right.
> I
> > used Replica exchange in two different system with the same input file
> but
> > here I get this error.
> > I used as input file for the analysis this file:
> >
> > #!/bin/bash
> >
> > cpptraj AVP_open.prmtop <<EOF
> > trajin remd.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r2.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r3.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r4.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r5.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r6.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r7.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r8.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r9.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r10.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r11.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r12.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r13.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r14.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r15.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r16.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r17.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r18.mdcrd.001 remdtraj remdtrajtemp 302.28
> > trajin remd_r19.mdcrd.001 remdtraj remdtrajtemp 302.28
> >
> > trajout remd_300K.mdcrd nobox
> > go
> > EOF
> >
> >
> > I am so confused,
> >
> > Do you have any idea?
> >
> > Thank you in advance,
> >
> > Nawel
> > ________________________________________
> > De : Mele N. [nm10g13.soton.ac.uk]
> > Envoyé : vendredi 4 juillet 2014 21:22
> > À : AMBER Mailing List
> > Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the
> > replica trajectories
> >
> > Thanks you very much for your help,
> > I will try it tomorrow and let you know if it work.
> >
> > ________________________________________
> > De : Jason Swails [jason.swails.gmail.com]
> > Envoyé : vendredi 4 juillet 2014 20:58
> > À : AMBER Mailing List
> > Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the
> > replica trajectories
> >
> > On Fri, Jul 4, 2014 at 12:23 PM, Mele N. <nm10g13.soton.ac.uk> wrote:
> >
> > > Thanks a lot for your answer,
> > >
> > > Actually I have a number of run for each replica, so you mean that just
> > by
> > > providing the lowest replica it will recognized even all the different
> > run?
> > >
> >
> > No. You need to provide the lowest replica number for _each_ run on a
> > separate trajin or ensemble line.
> >
> >
> > >
> > > By the way I used amber12 , does it change the way to analyse the
> > > temperature trajectories compare to Amber14?
> > >
> >
> > No difference.
> >
> > For example:
> >
> > trajin run1.mdcrd.000
> > trajin run2.mdcrd.000
> > trajin run3.mdcrd.000
> > ...
> >
> > Assuming you named your files run1.mdcrd.000, run1.mdcrd.001,
> > run.mdcrd.002, ... etc for the first run and then changed "run1" to
> "run2"
> > for the second run, etc.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
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> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jul 08 2014 - 20:00:02 PDT
